You should be able to manually change your config files (/includes/configure.php and /admin/includes/configure.php) to use the correct paths easily enough.

I suspect that you probably left the default values in there on installation, or got them wrong when you installed.

Around line 23 on /includes/configure.php, this will allow your root to serve the main Zen page:

define('DIR_WS_CATALOG', '/');

and around line 39 you'll need the physical path:

define('DIR_FS_CATALOG', '/path/to/website/');

(I don't follow the typical conventions on this, and I don't recall what the conventional path is, but that should be easy enough to figure out.)

Make similar changes for your admin config file.